readSCP {scp} | R Documentation

## Read single-cell proteomics data as a QFeatures object from tabular data and metadata

### Description

Convert tabular quantitative MS data and metadata from a spreadsheet or a `data.frame` into a QFeatures object containing SingleCellExperiment objects.

### Usage

    readSCP(
      featureData,
      colData,
      batchCol,
      channelCol,
      suffix = NULL,
      removeEmptyCols = FALSE,
      verbose = TRUE,
      ...
    )

### Arguments

`featureData` | File or object holding the quantitative data. Can be either a `character(1)` with the path to a text-based spreadsheet (comma-separated values by default, but see `...`) or an object that can be coerced to a `data.frame`. It is advised not to encode characters as factors.
`colData` | A `data.frame` or any object that can be coerced to a `data.frame`. `colData` is expected to contains all the sample meta information. Required fields are the acquisition batch (given by `batchCol`) and the acquisition channel within the batch (e.g. TMT channel, given by `channelCol`). Additional fields (e.g. sample type, acquisition date,...) are allowed and will be stored as sample meta data.
`batchCol` | A `numeric(1)` or `character(1)` pointing to the column of `featureData` and `colData` that contain the batch names. Make sure that the column name in both table are either identical and syntactically valid (if you supply a `character`) or have the same index (if you supply a `numeric`). Note that characters can be converted to syntactically valid names using `make.names`
`channelCol` | A `numeric(1)` or `character(1)` pointing to the column of `colData` that contains the column names of the quantitative data in `featureData` (see Example).
`suffix` | A `character()` giving the suffix of the column names in each assay. The length of the vector should equal the number of quantification channels and should contain unique character elements. If NULL, the names of the quantification columns in `featureData` are taken as suffix.
`removeEmptyCols` | A `logical(1)`. If true, the function will remove in each batch the columns that contain only missing values.
`verbose` | A `logical(1)` indicating whether the progress of the data reading and formatting should be printed to the console. Default is `TRUE`.
`...` | Further arguments that can be passed on to read.csv except `stringsAsFactors`, which is always `FALSE`.

### Value

An instance of class QFeatures. The expression data of each batch is stored in a separate assay as a SingleCellExperiment object.

### Note

The `SingleCellExperiment` class is built on top of the `RangedSummarizedExperiment` class. This means that some column names are forbidden in the `rowData`. Avoid using the following names: `seqnames`, `ranges`, `strand`, `start`, `end`, `width`, `element`

### Author(s)

Laurent Gatto, Christophe Vanderaa

### Examples

    ## Load an example table containing MaxQuant output
    data("mqScpData")

    ## Load the (user-generated) annotation table
    data("sampleAnnotation")

    ## Format the tables into a QFeatures object
    readSCP(featureData = mqScpData,
            colData = sampleAnnotation,
            batchCol = "Raw.file",
            channelCol = "Channel")

[Package scp version 1.4.0 Index]